"Andry Rajoelina is elected as the president of the republic of Madagascar and is taking his functions as soon as the swearing (in is conducted)," said court head Florent Rakotoarisoa. He received 58.96% of the votes cast, the court said.
The challenges to the electoral body's provisional count that were dismissed included one from the runner-up, lawmaker Siteny Randrianasoloniaiko. He got 14.39% of the vote, according to the court.
Ten out of 13 candidates boycotted the poll but their names were already on the ballot, leaving them to share the rest of the votes cast.
"The election took place peacefully, and it is proof that democracy in Madagascar and the Malagasy people have reached political maturity," Rajoelina told journalists outside the courtroom.
"There will be some changes but you don't change a winning team either," he said.
The Nov. 16 election was preceded by weeks of protests, with the opposition accusing Rajoelina of having created unfair election conditions, and the turn-out was less than 50%.
Rajoelina has dismissed allegations the vote was unfair and the army has warned against attempts to destabilise the country.
Nine foreign embassies, including the United States, United Kingdom and European Union, issued a joint statement "noting" the final results.
"In view of the tensions and incidents that characterised the electoral process, and the tense political context, it is now up to the newly-elected head of state, together with all the country's stakeholders, to take steps to restore confidence conducive to dialogue," the embassies said.
The opposition has said the 46.35% voter turn-out in the election was the lowest in the country's history.
Hajo Andrianainarivelo, a former minister among the candidates who boycotted the poll, has vowed to fight against what he said was a lack of respect for the laws of the land, and oppression of the people.
"The popular fight begins now," he said on Thursday.
Rajoelina, 49, first came to power in a 2009 coup. He stepped down in 2014 as leader of a transitional authority but then became president again after winning a 2018 election.